There are some great ideas coming up in this thread

I'll add another vote for Vincent/Yuffie. They'd make a neat duo, as they do in Dirge of Cerberus, and the throbbing sexual tension would keep people guessing too.

Hmm... how about Lulu and Cid Highwind? They're both serious, intelligent and mature, but Cid's recklessness and foul mouth would put him at odds with the quiet and sophisticated Black Mage.